This feature has been disabled in GWX, old story:
http://www.subsim.com/radioroom/showthread.php?t=103361
http://forums.ubi.com/eve/forums/a/t...3/m/3211059025
However, the so-called fix was made for the previous versions of GWX, and no-one has gone through the zones.cfg file in GWX2.1 to put it back in AFAIK.
It's a long time since I messed with this, since I play/mod SH4 these days, but if you create a backup of your zones.cfg, you can open the file with notepad and look for the sections of EngineRoom and FuelBunker of each vessel type. Some of them have been put to Critical=No. Just change it to Critical=Yes. That should bring the auto-aiming back. I can't remember right now, if that was all, which is needed...